[gmx-users] problems

David spoel at xray.bmc.uu.se
Tue Nov 30 18:45:31 CET 2004


On Tue, 2004-11-30 at 10:45 -0500, Lianqing Zheng wrote:
> Thanks, David. The same configuration runs 100+ ps in DL_POLY, but I'll
> check again if there are any conversion (from .xyz to pdb to gro)
> problems.
> 
> How about my second question about dihedral potential? Thanks!
Check with gmxdump

> 
> Lianqing
> 
> On Thu, 25 Nov 2004, David wrote:
> 
> >On Wed, 2004-11-24 at 16:30 -0500, Lianqing Zheng wrote:
> >> Dear GMX-pals,
> >> 
> >> I try to run NPT MD simulation of RDX and got a segmentation error for
> >> non-mpi version and "MPI process rank 0 (n0, p10908) caught a SIGSEGV."
> >> error for lam/mpi version. This happens when PME is turned on. When I use
> >> Cut-off, it gets stuck at step 5 and temperature becomes extremely high.
> >> 
> >sounds like a bad starting structure.
> >
> >> Another  question is about dihedral entries. If there are repeated
> >> entries, such as:
> >> 1 2 3 4 1 180.0 10.0 2
> >> 1 2 3 4 1 180.0  1.0 4
> >> 
> >> The results will be summation of these two or only the second? 
> >> 
> >> Thanks a lot!
> >> 
> >> Lianqing
> >> 
> >> 
> >> _______________________________________________
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> >-- 
> >David.
> >________________________________________________________________________
> >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >phone:  46 18 471 4205          fax: 46 18 511 755
> >spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >_______________________________________________
> >gmx-users mailing list
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> >http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
> 
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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